6-87472969-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The ENST00000369556(SLC35A1):​c.-35C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000216 in 615,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00024 ( 0 hom. )

Consequence

SLC35A1
ENST00000369556 5_prime_UTR

Scores

1
1

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.519
Variant links:
Genes affected
SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 6-87472969-C-T is Benign according to our data. Variant chr6-87472969-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 383493.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC35A1NM_006416.5 linkc.-35C>T upstream_gene_variant ENST00000369552.9 NP_006407.1 P78382-1
SLC35A1NM_001168398.2 linkc.-35C>T upstream_gene_variant NP_001161870.1 P78382-2
LOC124901357XR_007059668.1 linkn.-24G>A upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000213204ENST00000507897.5 linkn.*61-4393C>T intron_variant Intron 13 of 15 2 ENSP00000426769.1
SLC35A1ENST00000369552.9 linkc.-35C>T upstream_gene_variant 1 NM_006416.5 ENSP00000358565.4 P78382-1

Frequencies

GnomAD3 genomes
AF:
0.000145
AC:
22
AN:
152186
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000345
AC:
4
AN:
11578
Hom.:
0
AF XY:
0.000338
AC XY:
2
AN XY:
5918
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000634
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000240
AC:
111
AN:
463308
Hom.:
0
Cov.:
6
AF XY:
0.000230
AC XY:
56
AN XY:
243060
show subpopulations
Gnomad4 AFR exome
AF:
0.000100
Gnomad4 AMR exome
AF:
0.000104
Gnomad4 ASJ exome
AF:
0.0000806
Gnomad4 EAS exome
AF:
0.0000412
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000356
Gnomad4 NFE exome
AF:
0.000312
Gnomad4 OTH exome
AF:
0.000203
GnomAD4 genome
AF:
0.000145
AC:
22
AN:
152186
Hom.:
0
Cov.:
34
AF XY:
0.0000807
AC XY:
6
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.000121
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000277
Hom.:
0
Bravo
AF:
0.000234

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
May 21, 2018
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
13
DANN
Uncertain
0.99

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs373426456; hg19: chr6-88182687; API